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biopet.biopet
Commits
53ab6faa
Commit
53ab6faa
authored
Dec 04, 2015
by
Peter van 't Hof
Browse files
Added AssignTaxonomy step
parent
988be674
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
0 → 100644
View file @
53ab6faa
package
nl.lumc.sasc.biopet.extensions.qiime
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvan_thof on 12/4/15.
*/
class
AssignTaxonomy
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
executable
=
config
(
"exe"
,
default
=
"assign_taxonomy.py"
)
@Input
(
required
=
true
)
var
inputFasta
:
File
=
_
@Input
(
required
=
false
)
var
read_1_seqs_fp
:
Option
[
File
]
=
None
@Input
(
required
=
false
)
var
read_2_seqs_fp
:
Option
[
File
]
=
None
@Input
(
required
=
false
)
var
id_to_taxonomy_fp
:
Option
[
File
]
=
config
(
"id_to_taxonomy_fp"
)
@Input
(
required
=
false
)
var
reference_seqs_fp
:
Option
[
File
]
=
config
(
"reference_seqs_fp"
)
@Input
(
required
=
false
)
var
training_data_properties_fp
:
Option
[
File
]
=
config
(
"training_data_properties_fp"
)
var
single_ok
:
Boolean
=
config
(
"single_ok"
,
default
=
false
)
var
no_single_ok_generic
:
Boolean
=
config
(
"no_single_ok_generic"
,
default
=
false
)
var
amplicon_id_regex
:
Option
[
String
]
=
config
(
"amplicon_id_regex"
)
var
header_id_regex
:
Option
[
String
]
=
config
(
"header_id_regex"
)
var
assignment_method
:
Option
[
String
]
=
config
(
"assignment_method"
)
var
sortmerna_db
:
Option
[
String
]
=
config
(
"sortmerna_db"
)
var
sortmerna_e_value
:
Option
[
String
]
=
config
(
"sortmerna_e_value"
)
var
sortmerna_coverage
:
Option
[
String
]
=
config
(
"sortmerna_coverage"
)
var
sortmerna_best_N_alignments
:
Option
[
String
]
=
config
(
"sortmerna_best_N_alignments"
)
var
sortmerna_threads
:
Option
[
String
]
=
config
(
"sortmerna_threads"
)
var
blast_db
:
Option
[
String
]
=
config
(
"blast_db"
)
var
confidence
:
Option
[
String
]
=
config
(
"confidence"
)
var
min_consensus_fraction
:
Option
[
String
]
=
config
(
"min_consensus_fraction"
)
var
similarity
:
Option
[
String
]
=
config
(
"similarity"
)
var
uclust_max_accepts
:
Option
[
String
]
=
config
(
"uclust_max_accepts"
)
var
rdp_max_memory
:
Option
[
String
]
=
config
(
"rdp_max_memory"
)
var
blast_e_value
:
Option
[
String
]
=
config
(
"blast_e_value"
)
var
outputDir
:
File
=
_
def
versionCommand
=
executable
+
" --version"
def
versionRegex
=
"""Version: (.*)"""
.
r
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
outputDir
!=
null
)
}
def
cmdLine
=
executable
+
required
(
"-o"
,
inputFasta
)
+
optional
(
"--read_1_seqs_fp"
,
read_1_seqs_fp
)
+
optional
(
"--read_2_seqs_fp"
,
read_2_seqs_fp
)
+
optional
(
"-t"
,
id_to_taxonomy_fp
)
+
optional
(
"-r"
,
reference_seqs_fp
)
+
optional
(
"-p"
,
training_data_properties_fp
)
+
optional
(
"--amplicon_id_regex"
,
amplicon_id_regex
)
+
optional
(
"--header_id_regex"
,
header_id_regex
)
+
optional
(
"--assignment_method"
,
assignment_method
)
+
optional
(
"--sortmerna_db"
,
sortmerna_db
)
+
optional
(
"--sortmerna_e_value"
,
sortmerna_e_value
)
+
optional
(
"--sortmerna_coverage"
,
sortmerna_coverage
)
+
optional
(
"--sortmerna_best_N_alignments"
,
sortmerna_best_N_alignments
)
+
optional
(
"--sortmerna_threads"
,
sortmerna_threads
)
+
optional
(
"--blast_db"
,
blast_db
)
+
optional
(
"--confidence"
,
confidence
)
+
optional
(
"--min_consensus_fraction"
,
min_consensus_fraction
)
+
optional
(
"--similarity"
,
similarity
)
+
optional
(
"--uclust_max_accepts"
,
uclust_max_accepts
)
+
optional
(
"--rdp_max_memory"
,
rdp_max_memory
)
+
optional
(
"--blast_e_value"
,
blast_e_value
)
+
required
(
"--output_dir"
,
outputDir
)
}
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeR
a
tx.scala
→
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRt
a
x.scala
View file @
53ab6faa
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.BiopetQScript
import
nl.lumc.sasc.biopet.extensions.qiime.
{
PickRepSet
,
PickOtus
}
import
nl.lumc.sasc.biopet.extensions.qiime.
{
AssignTaxonomy
,
PickRepSet
,
PickOtus
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 12/4/15.
*/
class
GearsQiimeR
a
tx
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
class
GearsQiimeRt
a
x
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
var
fastaR1
:
File
=
_
var
fastqR2
:
Option
[
File
]
=
None
var
fastaR2
:
Option
[
File
]
=
None
override
def
fixedValues
=
Map
(
"assigntaxonomy"
->
Map
(
"assignment_method"
->
"rtax"
))
def
init
()
=
{
require
(
fastaR1
!=
null
)
...
...
@@ -31,5 +33,13 @@ class GearsQiimeRatx(val root: Configurable) extends QScript with BiopetQScript
pickRepSet
.
logFile
=
Some
(
new
File
(
pickRepSet
.
outputDir
,
fastaR1
.
getName
.
stripSuffix
(
".fasta"
).
stripSuffix
(
".fa"
).
stripSuffix
(
".fna"
)
+
".log"
))
add
(
pickRepSet
)
val
assignTaxonomy
=
new
AssignTaxonomy
(
this
)
assignTaxonomy
.
outputDir
=
new
File
(
outputDir
,
"assign_taxonomy"
)
assignTaxonomy
.
jobOutputFile
=
new
File
(
assignTaxonomy
.
outputDir
,
".assign_taxonomy.out"
)
assignTaxonomy
.
inputFasta
=
pickRepSet
.
outputFasta
.
get
assignTaxonomy
.
read_1_seqs_fp
=
Some
(
fastaR1
)
assignTaxonomy
.
read_2_seqs_fp
=
fastaR2
add
(
assignTaxonomy
)
}
}
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
53ab6faa
...
...
@@ -109,10 +109,10 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
}
if
(
gearsUserQiimeRtax
)
{
val
qiimeRatx
=
new
GearsQiimeR
a
tx
(
this
)
val
qiimeRatx
=
new
GearsQiimeRt
a
x
(
this
)
qiimeRatx
.
outputDir
=
new
File
(
outputDir
,
"qiime_ratx"
)
qiimeRatx
.
fastaR1
=
fastaR1
qiimeRatx
.
fast
q
R2
=
fastaR2
qiimeRatx
.
fast
a
R2
=
fastaR2
qiimeRatx
.
init
()
qiimeRatx
.
biopetScript
()
addAll
(
qiimeRatx
.
functions
)
...
...
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